DETERMINATION OF BASELINE FOR ANALYSIS

I am having challenges analysing my microarray data and i need assistance from anyone who could kindly offer me one.

I have sorted a cell population of interest (NUM CELLS) from mice infected with 2 different pathogens (PATHOGEN A and PATHOGEN H), purified RNA from the sorted cells and sent it to a company for RNA expression array. Naive mice do not express the cell population of interest (NUM CELLS).

My challenge is that, I have about 56,000 genes from these 2 pathogens (PATHOGEN A and PATHOGEN H) but do not know how to analyse my data since i have no baseline. My data is already normalised.

The company used Agilent technology and 1 colour array.

This is my first microarray experiment and I would really appreciate it if anyone could kindly explain how I should analyse my data. Any helpful reply would be greatly appreciated.

A useful question to ask yourself in these sorts of situations is: What question is the experiment designed to answer? If in your case the question is something along the line of "which genes are upregulated by infection with A and H?" Then you are probably out of luck as you need something to compare A and H to.

A useful question to ask yourself in these sorts of situations is: What question is the experiment designed to answer? If in your case the question is something along the line of "which genes are upregulated by infection with A and H?" Then you are probably out of luck as you need something to compare A and H to.

So... what is your hypothesis?

i am interested in knowing the genes that are upregulated or downregulated. thank you for your help